COFFEE_DIRS needs to check THEME_ROOT, if USE_CUSTOM_THEMES, and prepend that value to the basline COFFEE_DIRS list.   For example, see https://github.com/edx/edx-platform/pull/2387/files#diff-c88a6b22e27ad03d7d330b06a6c0d228R23 rakelib/assets.rake changes  --- that needs to be effected here also.